R Observatory: Metrics for geneset version 0.2.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

geneset

0.2.8Package record

Get Gene Sets for Gene Enrichment Analysis

1packages depend

5.4Kdownloads / year

18.0%test coverage

13/13flavors OK

Overview

About

Maintained by Yunze LiuCRAN page ↗GitHub ↗Issues ↗

Gene sets are fundamental for gene enrichment analysis. The package 'geneset' enables querying gene sets from public databases including 'GO' (Gene Ontology Consortium. (2004) doi:10.1093/nar/gkh036), 'KEGG' (Minoru et al. (2000) doi:10.1093/nar/28.1.27), 'WikiPathway' (Marvin et al. (2020) doi:10.1093/nar/gkaa1024), 'MsigDb' (Arthur et al. (2015) doi:10.1016/j.cels.2015.12.004), 'Reactome' (David et al. (2011) doi:10.1093/nar/gkq1018), 'MeSH' (Ish et al. (2014) doi:10.4103/0019-5413.139827), 'DisGeNET' (Janet et al. (2017) doi:10.1093/nar/gkw943), 'Disease Ontology' (Lynn et al. (2011) doi:10.1093/nar/gkr972), 'Network of Cancer Genes' (Dimitra et al. (2019) doi:10.1186/s13059-018-1612-0) and 'COVID-19' (Maxim et al. (2020) doi:10.21203/rs.3.rs-28582/v1). Gene sets are stored in the list object which provides data frame of 'geneset' and 'geneset_name'. The 'geneset' has two columns of term ID and gene ID. The 'geneset_name' has two columns of terms ID and term description.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("geneset", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("GangLiLab/geneset")

Development version from GangLiLab/geneset. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-geneset

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-geneset

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-geneset

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.0 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-01
ERROR12 OK, 1 ERROR2026-05-31
OK13 OK2026-05-21

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-05-20
OK14 OK2026-03-31
ERROR13 OK, 1 ERROR2026-03-30
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.8

READMEYes · 424 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9
Examples that run: 13%1 run in a plain check · 7 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

5.4K

CRAN downloads in the past year

Rank #4,897 · ~15/day · ~449/mo

Releases R versions

Daily download trend is not available in this view yet.

56130 days

1.7K90 days

5.4K1 year

Compare downloads with other packages →

Also on99 r2u7 autocran407 conda_forge

How downloads are counted

Repository

ganglilab/geneset ↗Organization: GangLiLab

12Stars

2Forks

1Open issues

1Open PRs

0Releases

34Commits

1Commit identities

enrichment-analysisgenegeneset-enrichment

License file reads as GPL-3.0 · 34 commits · Last activity 2026-07-27 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2025-06-19 · 92026-08-20 · 12

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/ganglilab/geneset on 2026-10-11.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing geneset adds 22 packages (15 with compiled code, 20 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, vctrs 1.0 MB.

Depends (1)

R >= 3.6

Imports (4)

dplyr RCurl fst stringr

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

genekitr

How these are counted

Code & Tests

Datasets

People & History

People (1)

Yunze Liu

Author, Maintainer since 0.2.6 (2022)

Releases (3)

Pick two releases to compare their code metrics.

0.2.8Latest
record
2026-07-27 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-11-20
0.2.7
record
2022-11-20 · diff ↗
archivedRemoved from CRAN
2022-11-11
policy violation On Internet access
0.2.6
record
2022-07-18
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-07-18
Total releases: 3 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6
Bundled data: 193 KB / 10 files
Download size: 210 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("geneset")

Format

Liu, Y. (2026). geneset: Get Gene Sets for Gene Enrichment Analysis (Version 0.2.8) [Computer software]. https://doi.org/10.32614/CRAN.package.geneset

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for geneset version 0.2.8 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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